#include "moldyn.h"
-#include "math/math.h"
-#include "init/init.h"
-#include "random/random.h"
-#include "visual/visual.h"
-#include "list/list.h"
-
-
int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
- //int ret;
-
- //ret=moldyn_parse_argv(moldyn,argc,argv);
- //if(ret<0) return ret;
-
memset(moldyn,0,sizeof(t_moldyn));
rand_init(&(moldyn->random),NULL,1);
return 0;
}
+int set_pressure(t_moldyn *moldyn,double p_ref) {
+
+ moldyn->p_ref=p_ref;
+
+ return 0;
+}
+
int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
moldyn->pt_scale=(ptype|ttype);
moldyn->dim.y=y;
moldyn->dim.z=z;
+ moldyn->volume=x*y*z;
+
if(visualize) {
moldyn->vis.dim.x=x;
moldyn->vis.dim.y=y;
moldyn->vis.dim.z=z;
}
- printf("[moldyn] dimensions in A:\n");
+ printf("[moldyn] dimensions in A and A^3 respectively:\n");
printf(" x: %f\n",moldyn->dim.x);
printf(" y: %f\n",moldyn->dim.y);
printf(" z: %f\n",moldyn->dim.z);
+ printf(" volume: %f\n",moldyn->volume);
printf(" visualize simulation box: %s\n",visualize?"on":"off");
return 0;
return 0;
}
+/*
+ * creating lattice functions
+ */
+
int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
u8 attr,u8 bnum,int a,int b,int c) {
return ret;
}
+/* fcc lattice init */
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+ int count;
+ int i,j;
+ t_3dvec o,r,n;
+ t_3dvec basis[3];
+ double help[3];
+ double x,y,z;
+
+ x=a*lc;
+ y=b*lc;
+ z=c*lc;
+
+ if(origin) v3_copy(&o,origin);
+ else v3_zero(&o);
+
+ /* construct the basis */
+ for(i=0;i<3;i++) {
+ for(j=0;j<3;j++) {
+ if(i!=j) help[j]=0.5*lc;
+ else help[j]=.0;
+ }
+ v3_set(&basis[i],help);
+ }
+
+ v3_zero(&r);
+ count=0;
+
+ /* fill up the room */
+ r.x=o.x;
+ while(r.x<x) {
+ r.y=o.y;
+ while(r.y<y) {
+ r.z=o.z;
+ while(r.z<z) {
+ v3_copy(&(atom[count].r),&r);
+ atom[count].element=1;
+ count+=1;
+ for(i=0;i<3;i++) {
+ v3_add(&n,&r,&basis[i]);
+ if((n.x<x+o.x)&&
+ (n.y<y+o.y)&&
+ (n.z<z+o.z)) {
+ v3_copy(&(atom[count].r),&n);
+ count+=1;
+ }
+ }
+ r.z+=lc;
+ }
+ r.y+=lc;
+ }
+ r.x+=lc;
+ }
+
+ /* coordinate transformation */
+ help[0]=x/2.0;
+ help[1]=y/2.0;
+ help[2]=z/2.0;
+ v3_set(&n,help);
+ for(i=0;i<count;i++)
+ v3_sub(&(atom[i].r),&(atom[i].r),&n);
+
+ return count;
+}
+
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+ int count;
+ t_3dvec o;
+
+ count=fcc_init(a,b,c,lc,atom,origin);
+
+ o.x=0.25*lc;
+ o.y=0.25*lc;
+ o.z=0.25*lc;
+
+ if(origin) v3_add(&o,&o,origin);
+
+ count+=fcc_init(a,b,c,lc,&atom[count],&o);
+
+ return count;
+}
+
int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
t_3dvec *r,t_3dvec *v) {
count+=1;
}
}
- if(count!=0) moldyn->t=(2.0*e)/(3.0*count*K_BOLTZMANN);
+ if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
else return 0; /* no atoms involved in scaling! */
/* (temporary) hack for e,t = 0 */
return 0;
}
+int scale_volume(t_moldyn *moldyn) {
+
+ t_atom *atom;
+ t_3dvec *dim,*vdim;
+ double virial,scale;
+ t_linkcell *lc;
+ int i;
+
+ atom=moldyn->atom;
+ dim=&(moldyn->dim);
+ vdim=&(moldyn->vis.dim);
+ lc=&(moldyn->lc);
+
+ for(i=0;i<moldyn->count;i++)
+ virial+=v3_norm(&(atom[i].virial));
+
+printf("%f\n",virial);
+ /* get pressure from virial */
+ moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*virial;
+ moldyn->p/=moldyn->volume;
+printf("%f\n",moldyn->p/(ATM));
+
+ /* scale factor */
+ if(moldyn->pt_scale&P_SCALE_BERENDSEN)
+ scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc);
+ else
+ /* should actually never be used */
+ scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0);
+
+printf("scale = %f\n",scale);
+ /* actual scaling */
+ dim->x*=scale;
+ dim->y*=scale;
+ dim->z*=scale;
+ if(vdim->x) vdim->x=dim->x;
+ if(vdim->y) vdim->y=dim->y;
+ if(vdim->z) vdim->z=dim->z;
+ moldyn->volume*=(scale*scale*scale);
+
+ /* check whether we need a new linkcell init */
+ if((dim->x/moldyn->cutoff!=lc->nx)||
+ (dim->y/moldyn->cutoff!=lc->ny)||
+ (dim->z/moldyn->cutoff!=lc->nx)) {
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn);
+ }
+
+ return 0;
+
+}
+
double get_e_kin(t_moldyn *moldyn) {
int i;
t_linkcell *lc;
int i;
- int fd;
-
- fd=open("/dev/null",O_WRONLY);
lc=&(moldyn->lc);
printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
for(i=0;i<lc->cells;i++)
- //list_init(&(lc->subcell[i]),1);
- list_init(&(lc->subcell[i]),fd);
+ list_init_f(&(lc->subcell[i]));
link_cell_update(moldyn);
int link_cell_update(t_moldyn *moldyn) {
int count,i,j,k;
- int nx,ny,nz;
+ int nx,ny;
t_atom *atom;
t_linkcell *lc;
+ double x,y,z;
atom=moldyn->atom;
lc=&(moldyn->lc);
nx=lc->nx;
ny=lc->ny;
- nz=lc->nz;
+
+ x=moldyn->dim.x/2;
+ y=moldyn->dim.y/2;
+ z=moldyn->dim.z/2;
for(i=0;i<lc->cells;i++)
- list_destroy(&(moldyn->lc.subcell[i]));
+ list_destroy_f(&(lc->subcell[i]));
for(count=0;count<moldyn->count;count++) {
- i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
- j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
- k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
- list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
- &(atom[count]));
+ i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
+ j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
+ k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
+ list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+ &(atom[count]));
}
return 0;
lc=&(moldyn->lc);
for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
- list_shutdown(&(moldyn->lc.subcell[i]));
+ list_destroy_f(&(moldyn->lc.subcell[i]));
+
+ free(lc->subcell);
return 0;
}
/* p/t scaling */
if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
scale_velocity(moldyn,FALSE);
+ if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
+ scale_volume(moldyn);
/* check for log & visualization */
if(e) {
v3_add(&(atom[i].v),&(atom[i].v),&delta);
}
-moldyn_bc_check(moldyn);
/* neighbour list update */
link_cell_update(moldyn);
t_linkcell *lc;
t_list neighbour_i[27];
t_list neighbour_i2[27];
- //t_list neighbour_j[27];
t_list *this,*that;
u8 bc_ij,bc_ik;
int dnlc;
/* reset energy */
moldyn->energy=0.0;
-
+
/* get energy and force of every atom */
for(i=0;i<count;i++) {
/* reset force */
v3_zero(&(itom[i].f));
+ /* reset viral of atom i */
+ v3_zero(&(itom[i].virial));
+
/* single particle potential/force */
if(itom[i].attr&ATOM_ATTR_1BP)
moldyn->func1b(moldyn,&(itom[i]));
for(j=0;j<27;j++) {
this=&(neighbour_i[j]);
- list_reset(this);
+ list_reset_f(this);
if(this->start==NULL)
continue;
for(k=0;k<27;k++) {
that=&(neighbour_i2[k]);
- list_reset(that);
+ list_reset_f(that);
if(that->start==NULL)
continue;
ktom,
bc_ik|bc_ij);
- } while(list_next(that)!=\
+ } while(list_next_f(that)!=\
L_NO_NEXT_ELEMENT);
}
jtom,bc_ij);
}
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
}
* periodic boundayr checking
*/
-int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
double x,y,z;
t_3dvec *dim;
if(a->z>=z) a->z-=dim->z;
else if(-a->z>z) a->z+=dim->z;
}
-printf("%f %f %f\n",a->x,x,a->x/x);
return 0;
}
s_r=S-R;
arg=M_PI*(d_ij-R)/s_r;
f_c=0.5+0.5*cos(arg);
- df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
+ //df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij)); /* MARK! */
+ df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
/* two body contribution (ij, ji) */
v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
/* tell 3bp that S > r > R */
s_r=S-R;
arg=M_PI*(d_ik-R)/s_r;
f_c_ik=0.5+0.5*cos(arg);
- df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
+ //df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik)); /* MARK */
+ df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
/* zeta_ij */
exchange->zeta_ij+=f_c_ik*g;
c2d2=exchange->cj2dj2;
/* cosine of theta_jik by scalaproduct */
- rr=v3_scalar_product(&dist_ij,&dist_jk); /* times -1 */
+ rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
dd=d_ij*d_jk;
cos_theta=rr/dd;
/* d_costheta */
- d_costheta1=1.0/(d_jk*d_ij);
- d_costheta2=cos_theta/(d_ij*d_ij); /* in fact -cos(), but ^ */
+ d_costheta1=1.0/dd;
+ d_costheta2=cos_theta/(d_ij*d_ij);
/* some usefull values */
h_cos=(h-cos_theta);
v3_add(&temp1,&temp1,&temp2);
v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
+ /* store dg in temp2 and use it for dVjk later */
+ v3_copy(&temp2,&temp1);
+
/* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
dzeta=&(exchange->dzeta_ji);
if(d_jk<R) {
/* zeta_ji */
exchange->zeta_ji+=f_c_jk*g;
- /* dzeta_ij */
+ /* dzeta_ji */
v3_scale(&temp1,&temp1,f_c_jk);
v3_add(dzeta,dzeta,&temp1);
}
/* dV_jk stuff | add force contribution on atom i immediately */
if(exchange->d_ij_between_rs) {
zeta=f_c*g;
- v3_scale(&temp1,&temp1,f_c);
- v3_scale(&temp2,&dist_ij,df_c);
- v3_add(&temp1,&temp1,&temp2);
+ v3_scale(&temp1,&temp2,f_c);
+ v3_scale(&temp2,&dist_ij,df_c*g);
+ v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
}
else {
zeta=g;
- // dzeta_jk is simply dg, which is temp1
+ // dzeta_jk is simply dg, which is stored in temp2
}
/* betajnj * zeta_jk ^ nj-1 */
tmp=exchange->betajnj*pow(zeta,(n-1.0));
- tmp=-chi/2.0*pow(1+tmp*zeta,-1.0/(2.0*n)-1)*tmp;
- v3_scale(&temp1,&temp1,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
- v3_add(&(ai->f),&(ai->f),&temp1); /* -1 skipped in f_a calc ^ */
+ tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
+ v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
+ v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
/* scaled with 0.5 ^ */
+
}
return 0;
t_atom *atom;
t_3dvec *dim;
int i;
+double x;
+u8 byte;
+int j,k;
atom=moldyn->atom;
dim=&(moldyn->dim);
+x=dim->x/2;
for(i=0;i<moldyn->count;i++) {
- if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2)
+ if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
printf("FATAL: atom %d: x: %.20f (%.20f)\n",
i,atom[i].r.x,dim->x/2);
+ printf("diagnostic:\n");
+ printf("-----------\natom.r.x:\n");
+ for(j=0;j<8;j++) {
+ memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
+ for(k=0;k<8;k++)
+ printf("%d%c",
+ ((byte)&(1<<k))?1:0,
+ (k==7)?'\n':'|');
+ }
+ printf("---------------\nx=dim.x/2:\n");
+ for(j=0;j<8;j++) {
+ memcpy(&byte,(u8 *)(&x)+j,1);
+ for(k=0;k<8;k++)
+ printf("%d%c",
+ ((byte)&(1<<k))?1:0,
+ (k==7)?'\n':'|');
+ }
+ if(atom[i].r.x==x) printf("the same!\n");
+ else printf("different!\n");
+ }
if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
printf("FATAL: atom %d: y: %.20f (%.20f)\n",
i,atom[i].r.y,dim->y/2);
return 0;
}
-
projects / physik / posic.git / blobdiff